def reMergeBamfiles(infiles, sentinal): infiles = [P.snip(x, ".sentinal") + ".bam" for x in infiles] outfile = P.snip(sentinal, ".sentinal") + ".bam" bad_samples = PARAMS["options_to_remove"].split(",") to_merge = IDR.filterBadLibraries(infiles, bad_samples) IDR.mergeBams(to_merge, outfile) P.touch(sentinal)
def poolSampleBamfiles(infiles, sentinal): """ Merge filtered sample files for each tissue """ infiles = [P.snip(x, ".sentinal") + ".bam" for x in infiles] outfile = P.snip(sentinal, ".sentinal") + ".bam" IDR.mergeBams(infiles, outfile) P.touch(sentinal)
def poolInputBamfiles(infiles, sentinal): """ Merge filtered input files for each tissue, with the option of excluding undesirable libraries. """ infiles = [P.snip(x, ".sentinal") + ".bam" for x in infiles] outfile = P.snip(sentinal, ".sentinal") + ".bam" bad_samples = PARAMS["filter_remove_inputs"].split(",") to_merge = IDR.filterBadLibraries(infiles, bad_samples) IDR.mergeBams(to_merge, outfile) P.touch(sentinal)
def poolInputBamfiles(infiles, sentinel): """ Merge filtered input files for each tissue, with the option of excluding undesirable libraries. """ infiles = [P.snip(x, ".sentinel") + ".bam" for x in infiles] outfile = P.snip(sentinel, ".sentinel") + ".bam" bad_samples = PARAMS["filter_remove_inputs"].split(",") if len(infiles) > 1: to_merge = IDR.filterBadLibraries(infiles, bad_samples) IDR.mergeBams(to_merge, outfile) else: os.symlink(os.path.abspath(infiles[0]), outfile) os.symlink(os.path.abspath(infiles[0]) + ".bai", outfile + ".bai") P.touch(sentinel)